OBJECTIVES: To estimate the prevalence of multimorbidity and to identify factors associated with it in the adult population from the metropolitan region of Manaus. DESIGN: Cross-sectional population-based study. SETTING: Interviews conducted between May and August of 2015 in eight cities that compose the metropolitan region of Manaus, Amazonas, Brazil. PARTICIPANTS: 4001 adults aged ≥18 years. PRIMARY OUTCOME MEASURES: Multimorbidity, measured by the occurrence of ≥2 and ≥3 chronic diseases, was the primary outcome. The associated factors were investigated by calculating the prevalence ratio (PR) obtained by Poisson regression, with robust adjustment of the variance in a hierarchical model. A factor analysis was conducted to investigate multimorbidity clusters. RESULTS: Half of the interviewees were women. The presence of a chronic disease was reported by 57.2% (95% CI 56.6% to 59.7%) of the interviewees, and the mean morbidity was 1.2 (1.1-1.2); 29.0% (95% CI 27.6% to 30.5%) reported ≥2 morbidities and 15.2% (95% CI 14.1% to 16.4%) reported ≥3 chronic conditions. Back pain was reported by one-third of the interviewees. Multimorbidity was highest in women, PR=1.66 (95% CI 1.50 to 1.83); the elderly, PR=5.68 (95% CI 4.51 to 7.15) and individuals with worse health perception, PR=3.70 (95% CI 2.73 to 5.00). Associated factors also included undergoing medical consultations, hospitalisation in the last year, suffering from dengue in the last year and seeking the same healthcare service. Factor analysis revealed a pattern of multimorbidity in women. The factor loading the most strength of association in women was heart disease. In men, an association was identified in two groups, and lung disease was the disease with the highest factorial loading. CONCLUSION: Multimorbidity was frequent in the metropolitan region of Manaus. It occurred most often in women, in the elderly and in those with worse health perception.